workspace-metabolism

MCP server and CLI for workspace metabolism: human-authored lifecycle rules keep agent workspaces useful across runs through policy-bounded cleanup, verified restore and an auditable history. Python 3.11+, zero dependencies, Windows / Linux / macOS.

▶️ Watch the 60-second GIF demo · try the interactive workspace-metabolism demo (download it and open it in a browser).

The problem

AI coding agents (Claude Code, Codex, DeepSeek Harness, …) share one thing — your workspace — and they leave a trail of scratch files, caches and staged directories behind. Nobody owns the cleanup: deleting by hand is irreversible, scheduled scripts have no audit trail, and the next agent run works in the garbage the last one left.

workspace-metabolism is the policy layer for that: one metabolism.json decides what every path is worth (G1 never touch → G4 auto), nothing is ever deleted by pattern — items move to a recycle area with per-file SHA-256 hashes and rollback restores them exactly — and every action lands in a hash-chained journal that verify can audit.

Try it in 30 seconds:

python -m pip install https://github.com/metabolism-tools/workspace-metabolism/releases/download/v0.8.0/workspace_metabolism-0.8.0-py3-none-any.whl
wm doctor --residue                  # what agent byproducts your policy doesn't govern yet
wm doctor --residue --apply-policy   # adopt the suggestions as policy entries (creates the file if missing)
wm audit                             # read-only checkup with health score

Distribution (v0.8.0): GitHub release and installable wheel. GitHub and PyPI publication are verified separately. Use the exact release wheel below. See v0.8.0 release notes for installation. The current source is 0.8.0. To run its recovery and maintenance checks from source, clone this release and run python -m pip install -e .. Use wm doctor --json to confirm the version, Python executable and module location actually in use. See upgrade notes. Listed in awesome-mcp-servers under Developer Tools (merged 2026-09-21). See the Glama tool-definition assessment for interface quality; it does not establish production reliability or lower supervision. Honest: no large production deployments yet, and the policy schema may shift before v1.0. Early adopters are welcome to break it on weird directory structures.

Honest boundaries — what this is not:

• Not a sandbox. wm gate is a governance/audit layer for cooperative agents; a compromised or malicious agent can bypass it and call the target server directly. OS-level sandboxing is a different layer.
• Not a heuristic classifier. It never decides "this file is garbage" on its own — only the policy you approved decides. doctor only suggests entries; nothing is governed until you adopt them.
• Does not fix agent bugs. It governs the byproducts agents leave; it does not stop agents from producing them.
• Local audit, not a notary. The hash-chained journal detects tampering with the tool's own records; it is not a distributed or court-grade ledger.

This repo has two linked ideas:

• Agentic Metabolic Engineering is the method: how to think about workspace lifecycle.
• AI governance as code is the implementation: how wm applies that method with policy files and commands.

中文快速上手（30 秒）

v0.6.0 新增：先认领再写入、清理避让未完成认领、精确绑定 SQLite 路径及不建库的只读 检查。复用现有任务和数据入口，不另建 AI 调度系统。见接入指南、 认领使用说明和数据库检查。

AI 编程（Claude Code / Codex / Aider 等）会在工作区留下大量草稿、缓存和 废弃文件，越堆越多，下一轮 AI 还得在垃圾堆里干活。这个工具用一份策略文件 管理文件的整个生命周期：检查（只读）→ 回收（可回滚）→ 验证（防篡改记录） → 清理。

python -m pip install https://github.com/metabolism-tools/workspace-metabolism/releases/download/v0.8.0/workspace_metabolism-0.8.0-py3-none-any.whl
python examples/demo.py                 # 已下载源码时可运行：盲删 vs 回收+回滚
wm init                                 # 生成策略文件 metabolism.json
wm audit                                # 只读体检，给文件贴营养标签
wm clean --grades G4 --yes              # 回收过期项（默认 dry-run，确认后加 --yes）
wm rollback <run_id>                    # 删错了？一键原样找回
wm govern write --path src/main.py      # 写文件前先问策略：允许吗？（AI 执行点拦截）
wm slim --db data/app.db --yes          # 数据库也会膨胀：策略驱动的库内瘦身（v0.3）

默认只读、绝不直接删文件；每步操作都有防篡改记录；Windows / Mac / Linux 通用。 项目处于早期，认领和受控编辑仍为实验能力；策略格式在 v1.0 前可能调整。完整英文文档见下文。

Why this exists

Most disk tools either show you space (ncdu, duf) or delete things (rmlint). workspace-metabolism is different: a policy file defines what every path is worth (grades G1–G4), and the tool only ever does what the policy allows — nothing more. It is the policy layer for multi-agent workspaces: Claude Code, Codex, Aider, OpenClaw and every other agent share one thing — your workspace — and the policy governs the byproducts all of them leave behind, regardless of which tool created them. It fixes no vendor and judges no file; see What this is not before you judge it.

• G1 never touch / G2 keep / G3 approve + reference check / G4 auto
• Deletion is never direct: items move to a recycle area, then rollback restores them after a per-file SHA-256 integrity check
• Every action lands in a hash-chained journal; verify detects any edit
• Read-only audit reports candidates, unregistered paths, disk alerts, growth trend and possible duplicates — plus residue on memory-backed mounts (tmpfs/ramfs: it costs RAM, not just disk)
• Optional protected window (e.g. trading hours, business hours) during which marked entries are never touched
• Scheduled runs are supported out of the box on Windows (Task Scheduler) and Linux/macOS (cron) via templates in examples/

Why not just a scheduled cleanup?

A scheduled task — or asking Codex to "clean up old files" on a timer — gets you at some point, files get removed. workspace-metabolism gets you:

• rules that live in the repo (metabolism.json), versioned and reviewable
• cleanup that never deletes directly: recycle area, per-file SHA-256, exact rollback
• a hash-chained journal that detects tampering
• the same behavior on every machine and every run, no AI judgment involved

Scheduling and metabolism are complementary, not rivals: this repo ships cron, Windows Task Scheduler and CI templates that run wm itself. The scheduler answers when; the policy answers what, how, and how to undo it.

What this is not

Four objections come up so often they deserve their own page (docs/positioning.md). The short version:

• Not a fix for vendor bugs — Claude Code's /tmp leak, OpenClaw's staged-dir residue: those belong upstream. We govern the workspace, which is the one thing every agent shares.
• Not a heuristic classifier — no guessing, no AI judgment. Only the policy file you wrote decides anything; wm explain <path> shows the rule.
• Not a rival to agent self-cleanup — agents should clean up after themselves; wm mcp + session-end hooks make that safe and audited.
• Not a blind-delete script — nothing is ever deleted by pattern: items move to a recycle area with per-file hashes, and rollback restores them. purge deletes file-recycle batches. The explicit retain policy can remove unreferenced database rows after writing a complete recovery export.

See it in action

This repo ships a reproducible benchmark: two identical workspaces run 30 simulated agent loops; one ends every loop with wm clean, the other never cleans. The result — 2 active files vs 242 — is a number you can reproduce yourself:

python examples/metabolism_benchmark.py

A recorded run (2026-08-16, wm 0.2.0) is in docs/publish/benchmark-run-20260816.json (raw log: docs/publish/benchmark-run-20260816.txt).

Case study: a 20.7 GB database that stalled a research engine

wm slim was born from a production incident, and the dogfooding round produced the most honest review the tool has had. Read docs/case-studies/research-engine-db-rot.md: three failure modes (dead work units, database rot, silently-dead jobs), the fixes, and what we found when we used wm slim to verify them — a policy stripping the wrong field, two path-matching bugs, a CLI flag-order pitfall that failed the first scheduled run, and the first successful run reclaiming 10.15 GB (21.7 GB → 11.3 GB) before uncovering a third real problem: the dead-position exclusion rule forgot itself once "clean" epochs diluted its learning window. Real usage is the final test.

🧬 Philosophy

workspace-metabolism treats your AI-generated workspace as a finite system: audit → clean → verify → rollback, with recyclable cleanup and a hash-chained audit trail. Cleanup is the means; metabolism is the frame. The one-liner: loops keep the agent running; metabolism keeps the workspace usable. We call this framing Agentic Metabolic Engineering — managing the byproducts of agent-driven software workspaces. Full write-up: docs/philosophy.md · the story · competitive analysis · academic anchors.

Quick start

# install the release that includes retain (PyPI is a separate channel)
pip install https://github.com/metabolism-tools/workspace-metabolism/releases/download/v0.8.0/workspace_metabolism-0.8.0-py3-none-any.whl

# or run without installing anything:
#   PYTHONPATH=src python -m workspace_metabolism --help

# try it on a throwaway workspace (builds demo files; shows the usual
# blind-delete fix vs the wm way: recycle + rollback + journal)
python examples/demo.py

Point the tool at your own workspace:

cd /path/to/workspace
wm init            # scaffold metabolism.json (like `git init`)
wm doctor          # check readiness before the first audit or cleanup
wm audit           # first checkup (read-only)
wm health          # workspace health score (0-100)
wm explain logs    # why a path is graded the way it is
wm clean --grades G4 --yes   # recycle expired G4 items (dry-run without --yes)
wm rollback <run_id>

wm init scans your workspace and registers common directories (source and docs as G2 keep, logs/tmp/cache as G4 auto, archive/staging as G3 approve). Edit metabolism.json and commit it like any source file. The tool auto-discovers metabolism.json (or .wm.json) in the workspace root, so --registry is optional. Nothing is cleaned unless it is registered in the policy file. Advanced users can start from examples/registry.example.json.

An executed clean that cannot move every planned item exits with an error. Its run manifest records both successful moves and failures, so successful moves can still be rolled back. The journal separates planned bytes from bytes actually moved and records zero reclaimed bytes: recycling does not free disk space. wm evidence reports these incomplete runs as failures.

Commands

Command	What it does
audit	Read-only health check; writes a report and a journal entry (also flags sensitive files and git-tracked content)
clean --grades G4	Move expired items to the recycle area (dry-run by default)
clean --grades G3	Same, but requires --approve + --approver
rollback <run_id>	Restore one cleanup run after an integrity check
purge --older-than 30	Delete expired file-recycle batches
retain --db data/objects.db	Preview removal of excess, unreferenced row versions under an explicit policy
retain --db data/objects.db --restore RUN_ID	Preview verified row restoration; add --yes to execute
verify	Check the journal hash chain and run manifests
status	Overview of workspace, recycle area and pending candidates
init	Scaffold a metabolism.json policy file (like git init)
explain <path>	Show what the policy says about a path (the nutrition label)
health	Workspace health score (0-100), with --json and --badge output
doctor	Read-only readiness check (workspace, policy, state, locks); --residue also lists common agent byproducts (.cursor, .claude, caches, logs) the policy does not govern yet — each with the exact policy entry that would govern it, --apply-policy adopts them
govern <action>	Check whether an AI action is allowed by policy and record the decision
gate --target ...	MCP governance proxy: every tool call of the wrapped server is checked against the policy first
slim --db PATH	Policy-driven in-place trimming of heavy JSON fields in a SQLite database (journaled; dry-run by default)
mcp	MCP stdio server so agents can run micro-metabolism themselves

Global flags:

Flag	Meaning
--root PATH	Workspace to govern (default: current directory)
--state-dir PATH	Journal / recycle / runs / reports (default: system cache directory, outside the workspace)
--registry PATH	Policy JSON (optional; auto-discovers metabolism.json / .wm.json)
--protected-window HH:MM-HH:MM	Weekday window; entries marked protected are skipped while active

The default state directory lives outside the workspace on purpose — a git add . in your project can never sweep the audit journal into version control.

wm doctor is a read-only preflight check. It reports whether the workspace and state directory are writable, whether the policy exists and is valid, and whether another wm operation currently holds the state lock. The lock serializes audits, cleanup, rollback and purge so concurrent scheduled or agent-triggered runs cannot interleave journal and recycle operations. It also reports interrupted recovery batches, the active installation, and the freshness and scope of explicitly registered maintenance receipts. See maintenance checks. Configuration alone does not establish that an executor has permission or completed its work.

AI governance as code

The optional ai_governance section is the concrete implementation of this repository's AI governance layer. It uses the same policy file to check AI actions before they happen. Unknown actions are denied by default; write actions can require a preview, while execute, delete and network actions can require a named approver. wm govern only makes and records a decision; it does not perform the action for the caller.

wm govern write --path src/main.py
wm govern write --path src/main.py --preview
wm govern execute --path scripts/release.ps1 --approve-by "name"
wm govern network --approve-by "name" --json

wm gate turns decisions into enforcement. It wraps any MCP stdio server and checks every tools/call against the policy before forwarding it; denied calls never reach the target and every decision lands in the journal:

wm gate --target "python -m my_mcp_server"

Map tool names to actions with tool_patterns (glob), e.g. "fs_write*": "write", "shell*": "execute". Unmatched tools default to the execute action. For tools whose calls carry a preview mode, pass "preview": true in the call arguments to satisfy requires_preview.

Every decision includes the policy hash and is written to the same hash-chained journal; govern returns a decision_id that clean / rollback / slim accept via --decision-id, so the journal shows the full intent → decision → execution chain. The approver value is an auditable declaration, not an authentication mechanism.

Honest boundary: wm gate is a governance and audit layer, not a sandbox. A compromised or malicious agent can bypass the proxy and talk to the target directly. Gate governs the cooperative agent; OS-level sandboxing governs the hostile one.

First run, guided: wm doctor --residue scans for the byproducts agents usually leave behind (.cursor, .claude, node_modules/.cache, __pycache__, logs …) that your policy does not govern yet. Every hit shows the exact policy entry that would govern it; --apply-policy adopts the suggestions into metabolism.json (creating it if needed). Nothing is ever deleted — the suggestions become policy, and the policy still decides everything afterwards:

wm doctor --residue               # what is ungoverned, and the suggested entries
wm doctor --residue --apply-policy  # adopt them as policy entries, then audit

Policy file

{
  "version": 1,
  "defaults": {
    "recycle_retention_days": 30,
    "max_item_mb": 2560,
    "disk_alert_free_gb": 20,
    "disk_alert_free_pct": 15,
    "dupe_scan_dirs": ["tmp", "cache"]
  },
  "never_clean": [".git", "README.md", "src"],
  "entries": [
    {"path": "logs", "grade": "G4", "cleanup": "auto", "retention_days": 30},
    {"path": "archive", "grade": "G3", "cleanup": "approve", "retention_days": 60},
    {"path": "**/__pycache__", "grade": "G4", "cleanup": "auto", "retention_days": 30}
  ]
}

Field	Meaning
path	Path or glob (*, **/) relative to --root
grade	G1 never / G2 keep / G3 approve / G4 auto
cleanup	never, auto or approve
retention_days	Idle days before the item becomes a candidate (required unless cleanup=never)
scope	Optional: files_only (top-level files of a directory)
protected	Optional: skip while a --protected-window is active
remote_authoritative	Optional: display marker for data with a remote source of truth
category	Optional free-form label for your own classification
owner	Optional: who is accountable for this rule
intent	Optional: why this rule exists
review_after	Optional: when this rule should be revisited

The policy format is versioned and validated against schema/metabolism.schema.json, so editors and agents can check your file before the tool does.

Health score

wm health combines the audit summary into one number from 0 to 100: 25 points for journal auditability, 25 for governance (unregistered paths, disk alerts), 35 for rot burden (expired candidates), and 15 for recycle readiness. Grades: A (90+), B (75+), C (60+), D (below).

wm health --json
wm health --badge   # shields.io endpoint JSON for a README badge

The badge above is generated from docs/health.json. A CI template that fails when the score drops below a threshold is in examples/ci-audit.yml.

Agents

wm mcp runs a zero-dependency MCP stdio server. Agents can init a policy, audit, explain, verify, and dry-run clean plans themselves; clean only executes when the caller explicitly passes execute=true, rollback restores a previous run from the recycle area (SHA-256 verified), and the policy file still decides everything. The end-of-loop ritual is automated in examples/micro_metabolism.py — wire it into a session-end hook so every loop ends with a checkup.

DeepSeek Harness (DSH)

DSH is an agent harness where everything is a plugin (Cordis). Its official third-party tool channel is MCP, and wm mcp already speaks it — one cordis.yml row exposes all nine wm tools to the DSH agent (audit, health, explain, verify, wm_db_check registered-SQLite checks, wm_govern pre-action policy checks, clean, init, rollback):

- insert:
    - id: workspace-metabolism
      name: '@deepseek-ai/dsh-mcp-client'
      config:
        serverName: wm
        transport: stdio
        command: wm
        args: [mcp]
        cwd: !!js process.cwd()

Full walkthrough (project cordis.yml vs --patch overlay, pinned --root/--state-dir, safety notes): docs/dsh-integration.md. A policy tuned for DSH-style workspaces (.agents/notes, scratch plugins, generated artifacts): examples/registry.dsh.example.json.

The optional Metabolic Maintenance skill plugin adds consequence-aware maintenance rules and downstream recovery verification to DSH's skill catalog. It loads instructions on demand and can pair with the MCP tools above. Download the plugin. Releases are also mirrored to the plugin's distribution repository, metabolism-tools/dsh-metabolic-maintenance, which carries the dsh-plugin topic so plugin directories can index it as a plugin.

Safety model

• clean is dry-run unless --yes is given.
• G4 needs --yes; G3 needs --approve and --approver (audit trail).
• Sensitive files are never auto-cleaned: audit flags secrets/keys/credentials (.env*, *.pem, *.key, *token*, *secret*, *credential*, id_rsa, …) in a dedicated report section, the policy validator refuses to register a sensitive path as G4 auto-clean, and clean skips any candidate that contains sensitive files.
• Git-aware classification: in a git repo, tracked files count as controlled by git (effectively G2) — they are excluded from the audit's unregistered list, and clean skips candidates that contain git-tracked files. Non-git workspaces fall back to pure policy matching. (Git is optional; wm never depends on it.)
• Items move to the recycle area with per-file SHA-256 hashes; rollback verifies them before restoring and refuses to overwrite an existing path.
• purge deletes file batches only inside the recycle area after retention.
• The journal is a hash chain; verify detects any tampering.

Scheduled runs

Templates with {{PLACEHOLDERS}} are in examples/:

• Windows — register_schedule.template.ps1: daily read-only audit (20:30), weekly G4 clean (Saturday 10:00), monthly purge (1st, 10:30).
• Linux/macOS — register_cron.template.sh: same schedule via cron.

Replace {{WM_CMD}}, {{ROOT}}, {{REGISTRY}}, {{STATE_DIR}} (and {{USER}} in cron) with your values. The scripts deliberately do not auto-detect your environment — your paths, your call.

Development

python -m pip install -e . pytest
python -m pytest

CI runs the full test suite on Ubuntu, Windows and macOS with Python 3.11 and 3.12. Issues are handled on weekends; pull requests are welcome.

Project family

Sister organization: Holdout — a toolchain against self-deception in quantitative research:

• falsification-ledger — pre-registration and falsification ledger
• factor-qc — fail-closed backtest quality gate
• pit-adjuster — PIT back-adjustment with drift detection
• lookahead-free — verifiable look-ahead-freedom checks
• ashare-data-immunity — data immunity for A-share daily bars
• lesson-book — tuition memory for traders

If workspace-metabolism keeps the workspace alive, Holdout keeps the research honest.

License

MIT

SQLite row retention

retain keeps the newest N versions per JSON group plus every referenced version, including references from old payloads. It never changes blob contents. The most specific workspace-relative entry must explicitly allow db_retain on a G2 database; G1, never_clean, active claims and --protected-window block execution. There are no CLI overrides that weaken the policy.

{
  "path": "data/objects.db", "grade": "G2", "cleanup": "never",
  "db_retain": {
    "table": "objects", "id_column": "hash", "blob_column": "body",
    "group_by": ["code", "month"], "order_column": "captured_at", "keep": 2,
    "blob_encoding": "gzip", "verify_sha256": true,
    "reference_paths": ["objects/*/*"]
  }
}

Here objects/*/* traverses a JSON dictionary of lists of object IDs in all rows. Missing optional fields contain no references; malformed containers, missing referenced rows, invalid JSON, hash mismatches, unsupported schema or exceeded budgets stop the operation. Ungrouped payload rows are always retained. An empty reference_paths explicitly asserts that rows have no in-table references. WM cannot discover undeclared or external consumers; policy authors must establish that boundary before authorizing deletion. Triggers, foreign-key relationships, generated columns and composite primary keys are not supported.

wm --root /workspace --registry policy.json retain --db data/objects.db
wm --root /workspace --registry policy.json retain --db data/objects.db --yes
wm --root /workspace --registry policy.json retain --db data/objects.db --restore retain-RUN_ID
wm --root /workspace --registry policy.json retain --db data/objects.db --restore retain-RUN_ID --yes

Use the actual run_id returned by the executed command. Preview writes no maintenance state. Execution plans inside a SQLite write transaction, exports all columns with their types, persists and reads back the export, then deletes. Recovery lives in <state-dir>/retention/<run_id>/, outside file purge's scope, with no automatic expiry. Keep it until downstream acceptance and recovery requirements are satisfied; do not reclaim these backups by age alone. An interrupted prepared batch blocks another retention run; inspect it and use --restore to reconcile it. Restoration verifies the export, original database identity and schema, and refuses to overwrite changed rows. Already identical rows are left alone, making an interrupted restore retryable. Hashes detect accidental changes, not malicious replacement of both export and manifest.

Defaults cap scans at 1,000,000 rows / 512 MiB encoded content / 120 seconds, decoded rows at 32 MiB and recovery export at 64 MiB. Policy can lower these limits. There is no automatic VACUUM, so reports claim zero disk reclamation; deleted database pages remain reusable inside SQLite, and recovery files consume space. Storage checks do not establish downstream business correctness. See tests/test_retain.py for reference protection, failure injection, concurrent writer exclusion, exact restoration and refusal of corrupted recovery material.

Trusted host integrations may supply a claim backend implementing transaction() and cleanup_claims() to the Python retain function. The backend must reuse the host's authoritative lock and retain active/unresolved scopes; the CLI never ignores a foreign registry. eligible_ids can only narrow WM's own safe candidates, and expected_ids_sha256 rejects a stale caller snapshot while the SQLite transaction is held.

Maintenance evidence (0.5.1)

wm --state-dir /path/to/state evidence prints a bounded, read-only JSON summary of journal.jsonl. Optionally add --observation check.json to read an existing check containing timezone-aware checked_at and boolean ok. No policy is required. Each input is limited to 8 MiB; no files are written.

Exit 0 means a nonempty internally consistent journal and, when requested, a readable valid check. It does not mean the system is healthy. Missing, empty, damaged, unsupported or oversized evidence returns exit 1. Time association does not establish matching scope, freshness, causality or business recovery. Human supervision, Token cost and net savings remain unknown. See case collection guide.

Safe recent-row retention (0.5.2)

slim can now match a real database relationship instead of assuming the ordering timestamp is embedded in every JSON payload:

"db_slim": {
  "table": "work_units",
  "blob_column": "payload_json",
  "strip_keys": ["regenerable_detail"],
  "protected_keys": ["consumer_evidence", "failure_reason"],
  "keep_recent": {
    "table": "epochs", "column": "created_at", "n": 3,
    "key_column": "epoch_id", "row_column": "epoch_id"
  },
  "vacuum_min_gb": 1.0
}

column sorts the reference table; key_column joins to the work table's row_column. Reference keys must be unique and non-null. For a row that would change, a missing relationship stops the whole plan before any update. The report's rows_kept_recent counts otherwise-modifiable rows protected by age. Policies that omit the two new columns retain legacy JSON matching, but missing or unknown references now stop instead of silently stripping the row. Migrate such policies before scheduled use. Protected keys are top-level JSON keys; conflicting CLI strip requests are rejected. This is not recursive field matching.

Execution holds the wm state lock and a SQLite write transaction across planning and updates. Preview opens the database read-only but still writes the existing wm journal. External writers must still observe the application's maintenance window; these locks do not validate consumer correctness or coordinate other systems. Backup/restore and post-maintenance consumer checks remain required.